Publications by authors named "Ian Clark"

Plant root and soil-associated microbiomes are influenced by niches, including bulk and rhizosphere soil. In this work, we collected bulk and rhizosphere soil samples at four potato developmental stages (leaf growth, flowering, tuber elongation and harvest) to identify whether rhizosphere microbiota are structured in a growth stage-dependent manner. The bacterial and fungal microbiota showed significant temporal differences in the rhizosphere and bulk soil.

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Nitroaromatic compounds are found in brown carbon aerosols emitted to the Earth's atmosphere by biomass burning, and are important organic chromophores for the absorption of solar radiation. Here, transient absorption spectroscopy spanning 100 fs-8 μs is used to explore the pH-dependent photochemical pathways for aqueous solutions of -nitrophenol, chosen as a representative nitroaromatic compound. Broadband ultrafast UV-visible and infrared probes are used to characterize the excited states and intermediate species involved in the multistep photochemistry, and to determine their lifetimes under different pH conditions.

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Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators.

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Article Synopsis
  • * In studies with miR-324-null mice, researchers found that these mice had increased bone density and thickness, reduced lipid content in bone marrow, and higher bone formation rates, indicating a strong connection between miR-324 and bone maintenance.
  • * It was revealed that miR-324-5p targets key regulators in bone cells, such as Pin1 and Runx2, which influence the balance between bone formation and resorption, highlighting the potential for miR-324-related therapies in treating bone diseases.
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  • Ammonia loss is most significant during high-temperature aerobic composting (>50°C), causing nitrogen depletion and environmental pollution.
  • A bacterial strain named LL-8 was found to efficiently convert ammonia nitrogen, reducing volatile ammonia loss by 42.9% in chicken manure composting when applied at elevated temperatures.
  • Whole-genome analysis of LL-8 indicated its ability to assimilate ammonium nitrogen, making it a promising solution for improving nitrogen content in compost and mitigating ammonia-related air pollution.
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  • The study examines how the evolution of wheat and the use of chemical fertilizers affect the beneficial bacteria that live on its roots.
  • It found that both the type of soil and the addition of fertilizers significantly influence the composition of these bacteria, with genetic changes in wheat also playing a role.
  • The research suggests that using fertilizers decreases the presence of helpful bacteria in modern wheat, which might affect plant growth and could inform future breeding programs aimed at improving crop yields.
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Mn-catalysed reactions offer great potential in synthetic organic and organometallic chemistry and the success of Mn carbonyl complexes as (pre)catalysts hinges on their stabilisation by strong field ligands enabling Mn(i)-based, redox neutral, catalytic cycles. The mechanistic processes underpinning the activation of the ubiquitous Mn(0) (pre)catalyst [Mn(CO)] in C-H bond functionalisation reactions is now reported for the first time. By combining time-resolved infra-red (TRIR) spectroscopy on a ps-ms timescale and studies using infra-red spectroscopy, insight into the microscopic bond activation processes which lead to the catalytic activity of [Mn(CO)] has been gained.

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Researchers who study the human hippocampus are naturally interested in how its subfields function. However, many researchers are precluded from examining subfields because their manual delineation from magnetic resonance imaging (MRI) scans (still the gold standard approach) is time consuming and requires significant expertise. To help ameliorate this issue, we present here two protocols, one for 3T MRI and the other for 7T MRI, that permit automated hippocampus segmentation into six subregions, namely dentate gyrus/cornu ammonis (CA)4, CA2/3, CA1, subiculum, pre/parasubiculum, and uncus along the entire length of the hippocampus.

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Nitroaromatic compounds are major constituents of the brown carbon aerosol particles in the troposphere that absorb near-ultraviolet (UV) and visible solar radiation and have a profound effect on the Earth's climate. The primary sources of brown carbon include biomass burning, forest fires, and residential burning of biofuels, and an important secondary source is photochemistry in aqueous cloud and fog droplets. Nitrobenzene is the smallest nitroaromatic molecule and a model for the photochemical behavior of larger nitroaromatic compounds.

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Background: To investigate best-corrected visual acuity (BCVA) outcomes in patients with optic nerve hypoplasia (ONH)/septo-optic-pituitary dysplasia (SOD). Our primary hypothesis was that BCVA in patients with ONH/SOD does not change significantly over time.

Methods: A chart review was undertaken in patients with a confirmed diagnosis of ONH/SOD.

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We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield.

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Background: Digital health technologies have potential to transform palliative care (PC) services. The global aging population poses unique challenges for PC, which digital health technologies may help overcome. Evaluation of attitudes and perceptions combined with quantification of prior use habits favor an understanding of psychological barriers to PC patient acceptance of digital health technologies including artificial intelligence (AI).

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Background: Optic nerve hypoplasia (ONH) and septo-optic-pituitary dysplasia (SOD) are neurodevelopmental disorders associated with congenital visual impairment. Our aim was to investigate associations between several ophthalmic and neuroimaging features in patients with ONH/SOD.

Methods: A retrospective chart and neuroimaging review was performed in patients with ONH/SOD.

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The pathologic assessment of colorectal carcinoma specimens plays a crucial role in the therapeutic management of patients and disease prognostication. The TNM staging system is used globally and is a critical component of colorectal carcinoma pathology reporting. However, our experience informs us that there are significant variations in the assignment of the TNM stage, both between pathologists and between hospital centers.

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Background: RNA editing at the Q/R site of GluA2 occurs with ~99% efficiency in the healthy brain, so that the majority of AMPARs contain GluA2(R) instead of the exonically encoded GluA2(Q). Reduced Q/R site editing infcreases AMPA receptor calcium permeability and leads to dendritic spine loss, neurodegeneration, seizures and learning impairments. Furthermore, GluA2 Q/R site editing is impaired in Alzheimer's disease (AD), raising the possibility that unedited GluA2(Q)-containing AMPARs contribute to synapse loss and neurodegeneration in AD.

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Over a decade's experience of post-stroke rehabilitation by administering the specific anti-TNF biological, etanercept, by the novel perispinal route, is consistent with a wide range of chronically diminished neurological function having been caused by persistent excessive cerebral levels of TNF. We propose that this TNF persistence, and cerebral disease chronicity, largely arises from a positive autocrine feedback loop of this cytokine, allowing the persistence of microglial activation caused by the excess TNF that these cells produce. It appears that many of these observations have never been exploited to construct a broad understanding and treatment of certain chronic, yet reversible, neurological illnesses.

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The nitrile containing Ru(II)polypyridyl complex [Ru(phen)(11,12-dCN-dppz)] () is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid and antiparallel G4s formed by the human telomer sequence d[AG(TTAG)]. Time-resolved infrared (TRIR) of upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-, Δ-, and Λ-/ binding, whereas Δ-/ binding is associated with interactions with thymine and adenine bases in the loop.

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Unlabelled: Agriculture faces potentially competing societal demands to produce food, fiber and fuel while reducing negative environmental impacts and delivering regulating, supporting and cultural ecosystem services. This necessitates a new generation of long-term agricultural field experiments designed to study the behavior of contrasting cropping systems in terms of multiple outcomes. We document the principles and practices of a new long-term experiment of this type at Rothamsted, established at two contrasting sites in 2017 and 2018, and report initial yield data at the crop and system level.

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We share data from N = 217 healthy adults (mean age 29 years, range 20-41; 109 females, 108 males) who underwent extensive cognitive assessment and neuroimaging to examine the neural basis of individual differences, with a particular focus on a brain structure called the hippocampus. Cognitive data were collected using a wide array of questionnaires, naturalistic tests that examined imagination, autobiographical memory recall and spatial navigation, traditional laboratory-based tests such as recalling word pairs, and comprehensive characterisation of the strategies used to perform the cognitive tests. 3 Tesla MRI data were also acquired and include multi-parameter mapping to examine tissue microstructure, diffusion-weighted MRI, T2-weighted high-resolution partial volume structural MRI scans (with the masks of hippocampal subfields manually segmented from these scans), whole brain resting state functional MRI scans and partial volume high resolution resting state functional MRI scans.

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An investigation into species formed following precatalyst activation in Mn-catalyzed C-H bond functionalization reactions is reported. Time-resolved infrared spectroscopy demonstrates that light-induced CO dissociation from precatalysts [Mn(C^N)(CO)] (C^N = cyclometalated 2-phenylpyridine (), cyclometalated 1,1-bis(4-methoxyphenyl)methanimine ()) in a toluene solution of 2-phenylpyridine () or 1,1-bis(4-methoxyphenyl)methanimine () results in the initial formation of solvent complexes -[Mn(C^N)(CO)(toluene)]. Subsequent solvent substitution on a nanosecond time scale then yields -[Mn(C^N)(CO)(κ-()-)] and -[Mn(C^N)(CO)(κ-()-)], respectively.

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Constraining the multiple climatic, lithological, topographic, and geochemical variables controlling isotope variations in large rivers is often challenging with standard statistical methods. Machine learning (ML) is an efficient method for analyzing multidimensional datasets, resolving correlated processes, and exploring relationships between variables simultaneously. We tested four ML algorithms to elucidate the controls of riverine δLi variations across the Yukon River Basin (YRB).

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The synergistic use of (organo)photoredox catalysts with hydrogen-atom transfer (HAT) cocatalysts has emerged as a powerful strategy for innate C(sp)-H bond functionalization, particularly for C-H bonds α- to nitrogen. Azide ion (N) was recently identified as an effective HAT catalyst for the challenging α-C-H alkylation of unprotected, primary alkylamines, in combination with dicyanoarene photocatalysts such as 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN). Here, time-resolved transient absorption spectroscopy over sub-picosecond to microsecond timescales provides kinetic and mechanistic details of the photoredox catalytic cycle in acetonitrile solution.

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Article Synopsis
  • Microbial catabolic activity (MCA) is a way to measure how microorganisms break down organic compounds in soil, which helps evaluate its microbial functionality.
  • Various methods exist for measuring MCA, with multi-substrate-induced respiration (MSIR) being highlighted for its ability to assess microbial function and diversity based on specific carbon sources.
  • The review compares techniques, emphasizes the effectiveness of MSIR in relation to agricultural practices and soil properties, and suggests using molecular tools alongside MSIR for improved measurement of MCA.
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People vary substantially in their capacity to recall past experiences, known as autobiographical memories. Here we investigated whether the volumes of specific hippocampal subfields were associated with autobiographical memory retrieval ability. We manually segmented the full length of the two hippocampi in 201 healthy young adults into DG/CA4, CA2/3, CA1, subiculum, pre/parasubiculum and uncus, in the largest such manually segmented subfield sample yet reported.

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The Sample Tubes on the Mars 2020 Perseverance rover were required to meet strict cleanliness standards for possible organic and inorganic contamination introduction to collected samples. There were also strict planetary protection cleanliness standards required to limit possible biological contamination. Together, these sets of standards also applied to associated hardware, like the Sample Tube hermetic seals.

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